How  Modern  Life  Depletes  Our  Gut  Microbes

Two studies give us a glimpse into our ancestors’ microbiome — you know, those trillions of bacteria that live in the human gut.

Image:  Maria Fabrizio for NPR

And the take-home message of the studies is clear: Western diets and modern-day hygiene have wiped a few dozen species right out of our digestive tracts. One missing microbe helps metabolize carbohydrates. Other bygone bacteria act as prebiotics. And another communicates with our immune system.

In other words, Americans’ digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.

“The concern is that we’re losing keystone species,” says microbiologist M. Gloria Dominguez-Bello, at the New York University School of Medicine. “That’s a hypothesis, but we haven’t proved it.”

Dominguez-Bello and her colleagues are the first to characterize the gut bacteria of people completely isolated from modern medicine, food and culture.

In 2009, her colleagues and a medical team with the Venezuelan government took a helicopter to a remote Yanomami tribe at the border of Venezuela and Brazil. Members of the tribe have lived as hunter-gatherers for more than 11,000 years in a mountainous area of the Amazon rain forest.

The visit was the first time that particular tribe had direct contact with modern society. “They knew about us, but we didn’t know about them,” Dominguez-Bello says. “They had names [in their language] for our helicopters and planes.”

Dominguez-Bello’s colleagues took samples from 12 of the villagers’ fecal matter. Back in New York City, the team used DNA analysis to figure out which species thrived in the hunter-gatherers’ guts.

The biggest surprise was how many different species were present in the Yanomami’s microbiome. The tribe had about 50 percent more ecological diversity than the average American has, Dominguez-Bello and her colleagues reported Friday in the journal Science Advances.

Continue to Article by  MICHAELEEN DOUCLEFF for NPR

Gut Microbes: The Final Digestive Frontier

It happens to all of us but don’t worry it’s completely natural. When food smells waft into our nostrils a host of physiological reactions occurs. We almost immediately begin to salivate (if not drool) and our stomach roars beckoning you to get a taste. These reactions are innate physiological properties of your digestive system that prepares your body for the food that it thinks you’re about to consume. Read more…

Photo Credit: Jimmy Sianipar & Anthony Martin

I present to you a colorful and vivid interpretation of gut flora of the small intestine, featuring E. Coli and a Ruminococcus bacteria. Both of these models were sculpted in Z-brush, as well as the microvilli you see in the foreground. The microvilli in the background were created using a hair and fur modifier in 3ds Max. All of these components were composited in Adobe Photoshop.

Perhaps the biggest challenge for this project were the microvilli, a seemingly odd thing to be concerned about, since they were not intended to be the focus of the piece. However, it’s the microvilli that contribute so much of the atmosphere and give you an anatomical reference for where this scene takes place, I wanted to make sure they were not glossed over. Thus, I created rolling hills of microvilli as far as the eye can see.

It is a striking idea that one of the keys to good health may turn out to involve managing our internal fermentation. Having recently learned to manage several external fermentations — of bread and kimchi and beer — I know a little about the vagaries of that process. You depend on the microbes, and you do your best to align their interests with yours, mainly by feeding them the kinds of things they like to eat — good “substrate.” But absolute control of the process is too much to hope for. It’s a lot more like gardening than governing.

The successful gardener has always known you don’t need to master the science of the soil, which is yet another hotbed of microbial fermentation, in order to nourish and nurture it. You just need to know what it likes to eat — basically, organic matter — and how, in a general way, to align your interests with the interests of the microbes and the plants. The gardener also discovers that, when pathogens or pests appear, chemical interventions “work,” that is, solve the immediate problem, but at a cost to the long-term health of the soil and the whole garden. The drive for absolute control leads to unanticipated forms of disorder.

This, it seems to me, is pretty much where we stand today with respect to our microbiomes — our teeming, quasi-wilderness. We don’t know a lot, but we probably know enough to begin taking better care of it. We have a pretty good idea of what it likes to eat, and what strong chemicals do to it. We know all we need to know, in other words, to begin, with modesty, to tend the unruly garden within.

Eating In

Your mom and your doctor both say you should eat more fiber. If you don’t, according to a new paper in Cell, your gut flora might consume you.

It sounds a bit like an old sci-fi movie plot, but researchers at the University of Michigan report that when normal, healthful bacteria in the gut don’t get the natural fiber they need to survive, they begin munching upon the layer of mucus lining the intestinal tract. Doing so can lead to weaknesses and holes exploited by dangerous, invasive bacteria and resulting infections.  

The research was conducted using specially raised mice that were born with no gut microbes of their own, allowing scientists to introduce and track specific combinations of microbes and diets. Mice fed a diet insufficient in fiber suffered declines in healthy, protective bacteria and increased infections from opportunistic pathogens.

“The lesson we’re learning from studying the interaction of fiber, gut microbes, and the intestinal barrier system is that if you don’t feed them, they can eat you,” said study author Eric Martens, associate professor of microbiology at the University of Michigan Medical School.

Gutopia: A Microbial Paradise

Gutopia is an idealized, homeostatic organ city of diverse symbiotic microbiota that is rich in fiber economy and free of any harmful pollutants. However, our dietary choices can tip the balance of this intestinal paradise and create a dystopic environmental suitable for the expansion of pathogenic microbes. Read more…

Illustration by Grace Danico

An interesting tidbit I learned from genetics and scientific journals (in layman's terms)

A study was done on mice. They took obese mice and healthy mice. The obese mice were on unhealthy diets and the healthy mice were on healthy diets.

They exchanged the gut flora (ie: the bacteria in your intestines that breaks down your food and allows you to absorb nutrients) between the mice so the obese mice had the healthy flora and the healthy mice had the obese flora. 

They kept their diets the same.

The healthy mice became temporarily obese and the obese mice became temporarily healthy… then they switched back to their original weights.

So… great… what does this mean? You need a gut flora transplant to help you lose weight? NOPE!!!!!!

What it means is so much cooler than that!!!! It means that eating healthy not only helps you lose weight for the obvious reasons, but it also means that continuing to eat healthy will help to cultivate the healthy gut flora and diminish the unhealthy gut flora. 

So the longer you eat healthy and the longer you go without eating junk, the less impact a weekend of party food will have on your body. Your system essentially will become more adept at digesting and absorbing healthy food and just passing unhealthy food right through without breaking it down.


Loving your stomach 101: be vigilant and persistent in tending your gut garden. probiotics to colonize the inner stomach garden with helpful bacteria and prebiotics to feed the bacteria species and help it proliferate and in turn process your foods more efficiently and ‘train’ your immune system how to target inconsistencies. also, since the useful component in garlic, allicin can kill bad bacteria and leave the good ones alone, it acts as a regulator of the gut flora so it would be wise to have an effective garlic supplement incorporated into tending after your stomach.

the best kind of probiotic out that scientists are okay with saying is effective and does what it advertises is yogurt, yeah apparently even more effective than pills (scientists are very reserved on their opinions about probiotics in general because it’s still in it’s early stages of research and marketed probiotics effects have been admittedly blown out of proportion). so do some h.w. on what probiotic yogurt best suits you and incorporate it into your diet and remember to think of what goes on in your stomach (and just overall body) as a community of bacteria that live with you and you need to have a good balance of useful bacteria living with you that can aid you, there’s many ways of going about this. like I said do some h.w. it’s worth the info if you’re about that 'loving yourself’ movement and considering all the things that can cause an imbalance of bacteria in your body.

Gut Bacteria & Gut Rumblings

At UCLA, researchers reveal another benefit of yogurt: probiotics found in yogurt can help improve brain function. Learn more about the world that probiotics occupy in a podcast about the “messy mystery in the middle of us” over at Radiolab. What we’re reading…